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Sánchez-Salvador A, González-de la Fuente S, Aguado B, Yates PA, Requena JM. Refinement of Leishmania donovani Genome Annotations in the Light of Ribosome-Protected mRNAs Fragments (Ribo-Seq Data). Genes (Basel) 2023; 14:1637. [PMID: 37628688 PMCID: PMC10454037 DOI: 10.3390/genes14081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Advances in next-generation sequencing methodologies have facilitated the assembly of an ever-increasing number of genomes. Gene annotations are typically conducted via specialized software, but the most accurate results require additional manual curation that incorporates insights derived from functional and bioinformatic analyses (e.g., transcriptomics, proteomics, and phylogenetics). In this study, we improved the annotation of the Leishmania donovani (strain HU3) genome using publicly available data from the deep sequencing of ribosome-protected mRNA fragments (Ribo-Seq). As a result of this analysis, we uncovered 70 previously non-annotated protein-coding genes and improved the annotation of around 600 genes. Additionally, we present evidence for small upstream open reading frames (uORFs) in a significant number of transcripts, indicating their potential role in the translational regulation of gene expression. The bioinformatics pipelines developed for these analyses can be used to improve the genome annotations of other organisms for which Ribo-Seq data are available. The improvements provided by these studies will bring us closer to the ultimate goal of a complete and accurately annotated L. donovani genome and will enhance future transcriptomics, proteomics, and genetics studies.
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Affiliation(s)
- Alejandro Sánchez-Salvador
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain; (S.G.-d.l.F.); (B.A.)
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain; (S.G.-d.l.F.); (B.A.)
| | - Phillip A. Yates
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jose M. Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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2
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Camacho E, González-de la Fuente S, Solana JC, Tabera L, Carrasco-Ramiro F, Aguado B, Requena JM. Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations. Genes (Basel) 2023; 14:genes14040866. [PMID: 37107624 PMCID: PMC10137940 DOI: 10.3390/genes14040866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023] Open
Abstract
Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins.
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Affiliation(s)
- Esther Camacho
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Jose Carlos Solana
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Tabera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Fernando Carrasco-Ramiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Jose M. Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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3
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Gómez-Liñán C, Gómez-Díaz E, Ceballos-Pérez G, Fernández-Moya S, Estévez AM. The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes. Nucleic Acids Res 2022; 50:12251-12265. [PMID: 36454008 PMCID: PMC9757043 DOI: 10.1093/nar/gkac1123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
In-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA polymerase II-derived transcripts that are produced from almost any genomic context. Pervasive RNAs are degraded by surveillance mechanisms, but the repertoire of proteins that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and in which initiation and termination of transcription occur at a limited number of sites per chromosome. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. We show here that depletion of RBP33 results in overexpression of ∼40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33-depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.
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Affiliation(s)
- Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Sandra M Fernández-Moya
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Antonio M Estévez
- To whom correspondence should be addressed. Tel: +34 958 181652; Fax: +34 958 181632;
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4
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Promastigote-to-Amastigote Conversion in Leishmania spp.—A Molecular View. Pathogens 2022; 11:pathogens11091052. [PMID: 36145483 PMCID: PMC9503511 DOI: 10.3390/pathogens11091052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
A key factor in the successful infection of a mammalian host by Leishmania parasites is their conversion from extracellular motile promastigotes into intracellular amastigotes. We discuss the physical and chemical triggers that induce this conversion and the accompanying changes at the molecular level crucial for the survival of these intracellular parasites. Special emphasis is given to the reliance of these trypanosomatids on the post-transcriptional regulation of gene expression but also to the role played by protein kinases, chaperone proteins and proteolytic enzymes. Lastly, we offer a model to integrate the transduction of different stress signals for the induction of stage conversion.
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Alonso A, Larraga J, Loayza FJ, Martínez E, Valladares B, Larraga V, Alcolea PJ. Stable Episomal Transfectant Leishmania infantum Promastigotes Over-Expressing the DEVH1 RNA Helicase Gene Down-Regulate Parasite Survival Genes. Pathogens 2022; 11:pathogens11070761. [PMID: 35890006 PMCID: PMC9323391 DOI: 10.3390/pathogens11070761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
The compartmentalization of untranslated mRNA molecules in granules occurring in many eukaryotic organisms including trypanosomatids involves the formation of complexes between mRNA molecules and RNA-binding proteins (RBPs). The putative ATP-dependent DEAD/H RNA helicase (DEVH1) from Leishmania infantum (Kinetoplastida: Trypanosomatidae) is one such proteins. The objective of this research is finding differentially expressed genes in a stable episomal transfectant L. infantum promastigote line over-expressing DEVH1 in the stationary phase of growth in axenic culture to get insight into the biological roles of this RNA helicase in the parasite. Interestingly, genes related to parasite survival and virulence factors, such as the hydrophilic surface protein/small hydrophilic endoplasmic reticulum protein (HASP/SHERP) gene cluster, an amastin, and genes related to reactive oxygen species detoxification are down-regulated in DEVH1 transfectant promastigotes.
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Affiliation(s)
- Ana Alonso
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Jaime Larraga
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Francisco Javier Loayza
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Enrique Martínez
- Department of Obstetrics and Gynecology, Pediatrics, Preventive Medicine and Public Health, Toxicology, Legal and Forensic Medicine and Parasitology, Faculty of Pharmacy, University Institute of Public Health of the Canary Islands (IUETSPC), University of La Laguna (ULL), Avda, Astrofísico Francisco, Sánchez s/n, Campus de Anchieta, 38207 La Laguna, Spain; (E.M.); (B.V.)
| | - Basilio Valladares
- Department of Obstetrics and Gynecology, Pediatrics, Preventive Medicine and Public Health, Toxicology, Legal and Forensic Medicine and Parasitology, Faculty of Pharmacy, University Institute of Public Health of the Canary Islands (IUETSPC), University of La Laguna (ULL), Avda, Astrofísico Francisco, Sánchez s/n, Campus de Anchieta, 38207 La Laguna, Spain; (E.M.); (B.V.)
| | - Vicente Larraga
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Pedro José Alcolea
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
- Correspondence: ; Tel.: +34-9-1837-3112; Fax: +34-9-1536-0432
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6
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Abdi Ghavidel A, Jajarmi V, Bandehpour M, Kazemi B. Polycistronic Expression of Multi-Subunit Complexes in the Eukaryotic Environment: A Narrative Review. IRANIAN JOURNAL OF PARASITOLOGY 2022; 17:286-295. [PMID: 36466018 PMCID: PMC9682371 DOI: 10.18502/ijpa.v17i3.10618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/15/2022] [Indexed: 06/17/2023]
Abstract
Protein complexes are involved in many vital biological processes. Therefore, researchers need these protein complexes for biochemical and biophysical studies. Several methods exist for expressing multi-subunit proteins in eukaryotic cells, such as 2A sequences, IRES, or intein. Nevertheless, each of these elements has several disadvantages that limit their usage. In this article, we suggest a new system for expressing multi-subunit proteins, which have several advantages over existing methods meanwhile it, lacks most of their disadvantages. Leishmania is a unicellular eukaryote and member of the Trypanosomatidae family. In the expression system of Leishmania, pre-long RNAs that contain several protein sequences transcribe. Then these long RNAs separate into mature mRNAs in the process named trans splicing. For producing multi-subunit protein, Leishmania transformed with a vector containing the sequences of all subunits. Therefore, those subunits translate and form the complex under eukaryotic cell conditions. The sequence of each protein must separate by the spatial sequence needed for trans splicing. Based on a Leishmania expression pattern, not only is it possible to produce the complexes with the correct structures and post-translational modifications, but also it is possible to overcome previous method problems.
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Affiliation(s)
- Afshin Abdi Ghavidel
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Jajarmi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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7
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Transcriptome Analysis of Intracellular Amastigotes of Clinical Leishmania infantum Lines from Therapeutic Failure Patients after Infection of Human Macrophages. Microorganisms 2022; 10:microorganisms10071304. [PMID: 35889023 PMCID: PMC9324091 DOI: 10.3390/microorganisms10071304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is considered to be one of the most neglected tropical diseases affecting humans and animals around the world. Due to the absence of an effective vaccine, current treatment is based on chemotherapy. However, the continuous appearance of drug resistance and therapeutic failure (TF) lead to an early obsolescence of treatments. Identification of the factors that contribute to TF and drug resistance in leishmaniasis will constitute a useful tool for establishing future strategies to control this disease. In this manuscript, we evaluated the transcriptomic changes in the intracellular amastigotes of the Leishmania infantum parasites isolated from patients with leishmaniasis and TF at 96 h post-infection of THP-1 cells. The adaptation of the parasites to their new environment leads to expression alterations in the genes involved mainly in the transport through cell membranes, energy and redox metabolism, and detoxification. Specifically, the gene that codes for the prostaglandin f2α synthase seems to be relevant in the pathogenicity and TF since it appears substantially upregulated in all the L. infantum lines. Overall, our results show that at the late infection timepoint, the transcriptome of the parasites undergoes significant changes that probably improve the survival of the Leishmania lines in the host cells, contributing to the TF phenotype as well as drug therapy evasion.
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8
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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Silveira GO, Coelho HS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs as possible therapeutic targets in protozoa, and in Schistosoma and other helminths. Parasitol Res 2021; 121:1091-1115. [PMID: 34859292 DOI: 10.1007/s00436-021-07384-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/14/2021] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) emerged in the past 20 years due to massive amounts of scientific data regarding transcriptomic analyses. They have been implicated in a plethora of cellular processes in higher eukaryotes. However, little is known about lncRNA possible involvement in parasitic diseases, with most studies only detecting their presence in parasites of human medical importance. Here, we review the progress on lncRNA studies and their functions in protozoans and helminths. In addition, we show an example of knockdown of one lncRNA in Schistosoma mansoni, SmLINC156349, which led to in vitro parasite adhesion, motility, and pairing impairment, with a 20% decrease in parasite viability and 33% reduction in female oviposition. Other observed phenotypes were a decrease in the proliferation rate of both male and female worms and their gonads, and reduced female lipid and vitelline droplets that are markers for well-developed vitellaria. Impairment of female worms' vitellaria in SmLINC156349-silenced worms led to egg development deficiency. All those results demonstrate the great potential of the tools and methods to characterize lncRNAs as potential new therapeutic targets. Further, we discuss the challenges and limitations of current methods for studying lncRNAs in parasites and possible solutions to overcome them, and we highlight the future directions of this exciting field.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Helena S Coelho
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Murilo S Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, 05503-900, Brazil. .,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
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10
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Salloum T, Tokajian S, Hirt RP. Advances in Understanding Leishmania Pathobiology: What Does RNA-Seq Tell Us? Front Cell Dev Biol 2021; 9:702240. [PMID: 34540827 PMCID: PMC8440825 DOI: 10.3389/fcell.2021.702240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a vector-borne disease caused by a protozoa parasite from over 20 Leishmania species. The clinical manifestations and the outcome of the disease vary greatly. Global RNA sequencing (RNA-Seq) analyses emerged as a powerful technique to profile the changes in the transcriptome that occur in the Leishmania parasites and their infected host cells as the parasites progresses through their life cycle. Following the bite of a sandfly vector, Leishmania are transmitted to a mammalian host where neutrophils and macrophages are key cells mediating the interactions with the parasites and result in either the elimination the infection or contributing to its proliferation. This review focuses on RNA-Seq based transcriptomics analyses and summarizes the main findings derived from this technology. In doing so, we will highlight caveats in our understanding of the parasite's pathobiology and suggest novel directions for research, including integrating more recent data highlighting the role of the bacterial members of the sandfly gut microbiota and the mammalian host skin microbiota in their potential role in influencing the quantitative and qualitative aspects of leishmaniasis pathology.
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Robert P. Hirt
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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11
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Camacho E, González-de la Fuente S, Solana JC, Rastrojo A, Carrasco-Ramiro F, Requena JM, Aguado B. Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain. Genes (Basel) 2021; 12:genes12091359. [PMID: 34573340 PMCID: PMC8468144 DOI: 10.3390/genes12091359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.
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12
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Medina J, Cruz-Saavedra L, Patiño LH, Muñoz M, Ramírez JD. Comparative analysis of the transcriptional responses of five Leishmania species to trivalent antimony. Parasit Vectors 2021; 14:419. [PMID: 34419127 PMCID: PMC8380399 DOI: 10.1186/s13071-021-04915-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmaniasis is a neglected tropical disease caused by several species of Leishmania. The resistance phenotype of these parasites depends on the characteristics of each species, which contributes to increased therapeutic failures. Understanding the mechanism used by the parasite to survive under treatment pressure in order to identify potential common and specific therapeutic targets is essential for the control of leishmaniasis. The aim of this study was to investigate the expression profiles and potential shared and specific resistance markers of the main Leishmania species of medical importance [subgenus L. (Leishmania): L. donovani, L. infantum and L. amazonensis; subgenus L. (Viannia): L. panamensis and L. braziliensis)] resistant and sensitive to trivalent stibogluconate (SbIII). METHODS We conducted comparative analysis of the transcriptomic profiles (only coding sequences) of lines with experimentally induced resistance to SbIII from biological replicates of five Leishmania species available in the databases of four articles based on ortholog attribution. Simultaneously, we carried out functional analysis of ontology and reconstruction of metabolic pathways of the resulting differentially expressed genes (DEGs). RESULTS Resistant lines for each species had differential responses in metabolic processes, compound binding, and membrane components concerning their sensitive counterpart. One hundred and thirty-nine metabolic pathways were found, with the three main pathways comprising cysteine and methionine metabolism, glycolysis, and the ribosome. Differentially expressed orthologous genes assigned to species-specific responses predominated, with 899 self-genes. No differentially expressed genes were found in common among the five species. Two common upregulated orthologous genes were found among four species (L. donovani, L. braziliensis, L. amazonensis, and L. panamensis) related to an RNA-binding protein and the NAD(P)H cytochrome-B5-oxidoreductase complex, associated with transcriptional control and de novo synthesis of linoleic acid, critical mechanisms in resistance to antimonials. CONCLUSION Herein, we identified potential species-specific genes related to resistance to SbIII. Therefore, we suggest that future studies consider a treatment scheme that is species-specific. Despite the limitations of our study, this is the first approach toward unraveling the pan-genus genetic mechanisms of resistance in leishmaniasis.
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Affiliation(s)
- Julián Medina
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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Ochoa R, Ortega-Pajares A, Castello FA, Serral F, Fernández Do Porto D, Villa-Pulgarin JA, Varela-M RE, Muskus C. Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. Biomolecules 2021; 11:biom11071037. [PMID: 34356660 PMCID: PMC8301987 DOI: 10.3390/biom11071037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022] Open
Abstract
Leishmaniasis is a public health disease that requires the development of more effective treatments and the identification of novel molecular targets. Since blocking the PI3K/AKT pathway has been successfully studied as an effective anticancer strategy for decades, we examined whether the same approach would also be feasible in Leishmania due to their high amount and diverse set of annotated proteins. Here, we used a best reciprocal hits protocol to identify potential protein kinase homologues in an annotated human PI3K/AKT pathway. We calculated their ligandibility based on available bioactivity data of the reported homologues and modelled their 3D structures to estimate the druggability of their binding pockets. The models were used to run a virtual screening method with molecular docking. We found and studied five protein kinases in five different Leishmania species, which are AKT, CDK, AMPK, mTOR and GSK3 homologues from the studied pathways. The compounds found for different enzymes and species were analysed and suggested as starting point scaffolds for the design of inhibitors. We studied the kinases’ participation in protein–protein interaction networks, and the potential deleterious effects, if inhibited, were supported with the literature. In the case of Leishmania GSK3, an inhibitor of its human counterpart, prioritized by our method, was validated in vitro to test its anti-Leishmania activity and indirectly infer the presence of the enzyme in the parasite. The analysis contributes to improving the knowledge about the presence of similar signalling pathways in Leishmania, as well as the discovery of compounds acting against any of these kinases as potential molecular targets in the parasite.
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Affiliation(s)
- Rodrigo Ochoa
- Programa de Estudio y Control de Enfermedades Tropicales PECET, Faculty of Medicine, University of Antioquia, Medellín 050010, Colombia;
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia, Medellín 050010, Colombia
- Correspondence: (R.O.); (R.E.V.-M.)
| | - Amaya Ortega-Pajares
- Department of Medicine, The Peter Doherty Institute, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Florencia A. Castello
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), IC-CONICET Ciudad Universitaria, Pabellon 2, Ciudad de Buenos Aires C1428EHA, Argentina; (F.A.C.); (F.S.); (D.F.D.P.)
| | - Federico Serral
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), IC-CONICET Ciudad Universitaria, Pabellon 2, Ciudad de Buenos Aires C1428EHA, Argentina; (F.A.C.); (F.S.); (D.F.D.P.)
| | - Darío Fernández Do Porto
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), IC-CONICET Ciudad Universitaria, Pabellon 2, Ciudad de Buenos Aires C1428EHA, Argentina; (F.A.C.); (F.S.); (D.F.D.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria, Pabellon 2, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Janny A. Villa-Pulgarin
- Grupo de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín 050034, Colombia;
| | - Rubén E. Varela-M
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760035, Colombia
- Correspondence: (R.O.); (R.E.V.-M.)
| | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales PECET, Faculty of Medicine, University of Antioquia, Medellín 050010, Colombia;
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14
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Andrade JM, Gonçalves LO, Liarte DB, Lima DA, Guimarães FG, de Melo Resende D, Santi AMM, de Oliveira LM, Velloso JPL, Delfino RG, Pescher P, Späth GF, Ruiz JC, Murta SMF. Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines. Parasit Vectors 2020; 13:600. [PMID: 33256787 PMCID: PMC7706067 DOI: 10.1186/s13071-020-04486-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022] Open
Abstract
Background One of the major challenges to leishmaniasis treatment is the emergence of parasites resistant to antimony. To study differentially expressed genes associated with drug resistance, we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing. Methods All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search. Results The analytical pipeline considering an adjusted p-value < 0.05 and fold change > 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the gene ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host–parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation. Conclusions The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with the antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.![]()
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Affiliation(s)
- Juvana Moreira Andrade
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Leilane Oliveira Gonçalves
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.,Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Davi Alvarenga Lima
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.,Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | | | - Daniela de Melo Resende
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.,Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Ana Maria Murta Santi
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Luciana Marcia de Oliveira
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Paris, France
| | | | - Renato Guimarães Delfino
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Pascale Pescher
- Unité de Parasitologie moléculaire et Signalisation, Département de Parasitologie et Mycologie, Institut Pasteur, Paris, France
| | - Gerald F Späth
- Unité de Parasitologie moléculaire et Signalisation, Département de Parasitologie et Mycologie, Institut Pasteur, Paris, France
| | - Jeronimo Conceição Ruiz
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil. .,Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil.
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15
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Patino LH, Muñoz M, Cruz-Saavedra L, Muskus C, Ramírez JD. Genomic Diversification, Structural Plasticity, and Hybridization in Leishmania (Viannia) braziliensis. Front Cell Infect Microbiol 2020; 10:582192. [PMID: 33178631 PMCID: PMC7596589 DOI: 10.3389/fcimb.2020.582192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/28/2020] [Indexed: 01/12/2023] Open
Abstract
Leishmania (Viannia) braziliensis is an important Leishmania species circulating in several Central and South American countries. Among Leishmania species circulating in Brazil, Argentina and Colombia, L. braziliensis has the highest genomic variability. However, genomic variability at the whole genome level has been only studied in Brazilian and Peruvian isolates; to date, no Colombian isolates have been studied. Considering that in Colombia, L. braziliensis is a species with great clinical and therapeutic relevance, as well as the role of genetic variability in the epidemiology of leishmaniasis, we analyzed and evaluated intraspecific genomic variability of L. braziliensis from Colombian and Bolivian isolates and compared them with Brazilian isolates. Twenty-one genomes were analyzed, six from Colombian patients, one from a Bolivian patient, and 14 Brazilian isolates downloaded from public databases. The results obtained of Phylogenomic analysis showed the existence of four well-supported clades, which evidenced intraspecific variability. The whole-genome analysis revealed structural variations in the somy, mainly in the Brazilian genomes (clade 1 and clade 3), low copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs) in all genomes analyzed. Interestingly, the genomes belonging to clades 2 and 3 from Colombia and Brazil, respectively, were characterized by low heterozygosity (~90% of SNP loci were homozygous) and regions suggestive of loss of heterozygosity (LOH). Additionally, we observed the drastic whole genome loss of heterozygosity and possible hybridization events in one genome belonging to clade 4. Unique/shared SNPs between and within the four clades were identified, revealing the importance of some of them in biological processes of L. braziliensis. Our analyses demonstrate high genomic variability of L. braziliensis in different regions of South America, mainly in Colombia and suggest that this species exhibits striking genomic diversity and a capacity of genomic hybridization; additionally, this is the first study to report whole-genome sequences of Colombian L. braziliensis isolates.
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Affiliation(s)
- Luz H Patino
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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16
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Herreros-Cabello A, Callejas-Hernández F, Gironès N, Fresno M. Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications. Genes (Basel) 2020; 11:E1196. [PMID: 33066599 PMCID: PMC7602482 DOI: 10.3390/genes11101196] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 01/20/2023] Open
Abstract
Chagas disease caused by the parasite Trypanosoma cruzi affects millions of people. Although its first genome dates from 2005, its complexity hindered a complete assembly and annotation. However, the new sequencing methods have improved genome annotation of some strains elucidating the broad genetic diversity and complexity of this parasite. Here, we reviewed the genomic structure and regulation, the genetic diversity, and the analysis of the principal multi-gene families of the recent genomes for several strains. The telomeric and sub-telomeric regions are sites with high recombination events, the genome displays two different compartments, the core and the disruptive, and the genome plasticity seems to play a key role in the survival and the infection process. Trypanosoma cruzi (T. cruzi) genome is composed mainly of multi-gene families as the trans-sialidases, mucins, and mucin-associated surface proteins. Trans-sialidases are the most abundant genes in the genome and show an important role in the effectiveness of the infection and the parasite survival. Mucins and MASPs are also important glycosylated proteins of the surface of the parasite that play a major biological role in both insect and mammal-dwelling stages. Altogether, these studies confirm the complexity of T. cruzi genome revealing relevant concepts to better understand Chagas disease.
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Affiliation(s)
- Alfonso Herreros-Cabello
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
| | - Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
- Instituto Sanitario de Investigación Princesa, 28006 Madrid, Spain
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (A.H.-C.); (F.C.-H.)
- Instituto Sanitario de Investigación Princesa, 28006 Madrid, Spain
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17
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Aoki JI, Muxel SM, Laranjeira-Silva MF, Zampieri RA, Müller KE, Nerland AH, Floeter-Winter LM. Dual transcriptome analysis reveals differential gene expression modulation influenced by Leishmania arginase and host genetic background. Microb Genom 2020; 6:mgen000427. [PMID: 32886592 PMCID: PMC7643972 DOI: 10.1099/mgen.0.000427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 01/04/2023] Open
Abstract
The outcome of Leishmania infection is strongly influenced by the host's genetic background. BALB/c mice are susceptible to Leishmania infection, while C57BL/6 mice show discrete resistance. Central to the fate of the infection is the availability of l-arginine and the related metabolic processes in the host and parasite. Depending on l-arginine availability, nitric oxide synthase 2 (NOS2) of the host cell produces nitric oxide (NO) controlling the parasite growth. On the other hand, Leishmania can also use host l-arginine for the production of polyamines through its own arginase activity, thus favouring parasite replication. Considering RNA-seq data, we analysed the dual modulation of host and parasite gene expression of BALB/c or C57BL/6 mouse bone marrow-derived macrophages (BMDMs) after 4 h of infection with Leishmania amazonensis wild-type (La-WT) or L. amazonensis arginase knockout (La-arg-). We identified 12 641 host transcripts and 8282 parasite transcripts by alignment analysis with the respective Mus musculus and L. mexicana genomes. The comparison of BALB/c_La-arg-versus BALB/c_La-WT revealed 233 modulated transcripts, with most related to the immune response and some related to the amino acid transporters and l-arginine metabolism. In contrast, the comparison of C57BL/6_La-arg-vs. C57BL/6_La-WT revealed only 30 modulated transcripts, including some related to the immune response but none related to amino acid transport or l-arginine metabolism. The transcriptome profiles of the intracellular amastigote revealed 94 modulated transcripts in the comparison of La-arg-_BALB/c vs. La-WT_BALB/c and 45 modulated transcripts in the comparison of La-arg-_C57BL/6 vs. La-WT_C57BL/6. Taken together, our data present new insights into the impact of parasite arginase activity on the orchestration of the host gene expression modulation, including in the immune response and amino acid transport and metabolism, mainly in susceptible BALB/c-infected macrophages. Moreover, we show how parasite arginase activity affects parasite gene expression modulation, including amino acid uptake and amastin expression.
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Affiliation(s)
- Juliana Ide Aoki
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | - Sandra Marcia Muxel
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | | | | | - Karl Erik Müller
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Internal Medicine, Drammen Hospital, Drammen, Norway
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18
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Acuña SM, Floeter-Winter LM, Muxel SM. MicroRNAs: Biological Regulators in Pathogen-Host Interactions. Cells 2020; 9:E113. [PMID: 31906500 PMCID: PMC7016591 DOI: 10.3390/cells9010113] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022] Open
Abstract
An inflammatory response is essential for combating invading pathogens. Several effector components, as well as immune cell populations, are involved in mounting an immune response, thereby destroying pathogenic organisms such as bacteria, fungi, viruses, and parasites. In the past decade, microRNAs (miRNAs), a group of noncoding small RNAs, have emerged as functionally significant regulatory molecules with the significant capability of fine-tuning biological processes. The important role of miRNAs in inflammation and immune responses is highlighted by studies in which the regulation of miRNAs in the host was shown to be related to infectious diseases and associated with the eradication or susceptibility of the infection. Here, we review the biological aspects of microRNAs, focusing on their roles as regulators of gene expression during pathogen-host interactions and their implications in the immune response against Leishmania, Trypanosoma, Toxoplasma, and Plasmodium infectious diseases.
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Affiliation(s)
| | | | - Sandra Marcia Muxel
- Department of Physiology, Universidade de São Paulo, 05508-090 São Paulo, Brazil; (S.M.A.); (L.M.F.-W.)
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Differential immune response modulation in early Leishmania amazonensis infection of BALB/c and C57BL/6 macrophages based on transcriptome profiles. Sci Rep 2019; 9:19841. [PMID: 31882833 PMCID: PMC6934472 DOI: 10.1038/s41598-019-56305-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
The fate of Leishmania infection can be strongly influenced by the host genetic background. In this work, we describe gene expression modulation of the immune system based on dual global transcriptome profiles of bone marrow-derived macrophages (BMDMs) from BALB/c and C57BL/6 mice infected with Leishmania amazonensis. A total of 12,641 host transcripts were identified according to the alignment to the Mus musculus genome. Differentially expressed genes (DEGs) profiling revealed a differential modulation of the basal genetic background between the two hosts independent of L. amazonensis infection. In addition, in response to early L. amazonensis infection, 10 genes were modulated in infected BALB/c vs. non-infected BALB/c macrophages; and 127 genes were modulated in infected C57BL/6 vs. non-infected C57BL/6 macrophages. These modulated genes appeared to be related to the main immune response processes, such as recognition, antigen presentation, costimulation and proliferation. The distinct gene expression was correlated with the susceptibility and resistance to infection of each host. Furthermore, upon comparing the DEGs in BMDMs vs. peritoneal macrophages, we observed no differences in the gene expression patterns of Jun, Fcgr1 and Il1b, suggesting a similar activation trends of transcription factor binding, recognition and phagocytosis, as well as the proinflammatory cytokine production in response to early L. amazonensis infection. Analysis of the DEG profile of the parasite revealed only one DEG among the 8,282 transcripts, indicating that parasite gene expression in early infection does not depend on the host genetic background.
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20
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Callejas-Hernández F, Gutierrez-Nogues Á, Rastrojo A, Gironès N, Fresno M. Analysis of mRNA processing at whole transcriptome level, transcriptomic profile and genome sequence refinement of Trypanosoma cruzi. Sci Rep 2019; 9:17376. [PMID: 31758058 PMCID: PMC6874640 DOI: 10.1038/s41598-019-53924-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/07/2019] [Indexed: 12/16/2022] Open
Abstract
The genomic sequence of Trypanosoma cruzi, the protozoan causative of Chagas disease was published more than a decade ago. However, due to their complexity, its complete haploid predicted sequence and therefore its genetic repertoire remains unconfirmed. In this work, we have used RNAseq data to improve the previous genome assembly of Sylvio X10 strain and to define the complete transcriptome at trypomastigote stage (mammalian stage). A total of 22,977 transcripts were identified, of which more than half could be considered novel as they did not match previously annotated genes. Moreover, for the first time in T. cruzi, we are providing their relative abundance levels. We have identified that Sylvio X10 trypomastigotes exhibit a predominance of surface protein genes, specifically those encoding trans-sialidase and mucin-like proteins. On the other hand, detailed analysis of the pre-mRNA processing sites revealed some similarities but also some differences in the spliced leader and different polyadenylation addition sites compared to close related kinetoplastid parasites. Our results also confirm that transcription is bidirectional as occur in other kinetoplastids and the proportion of forward-sense and reverse-sense transcripts is almost equivalent, demonstrating that a strand-specificity does not exist.
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Affiliation(s)
- Francisco Callejas-Hernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Ángel Gutierrez-Nogues
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Núria Gironès
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
- Instituto Sanitario de Investigación Princesa, Madrid, Spain.
| | - Manuel Fresno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
- Instituto Sanitario de Investigación Princesa, Madrid, Spain.
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Orrego LM, Cabello-Donayre M, Vargas P, Martínez-García M, Sánchez C, Pineda-Molina E, Jiménez M, Molina R, Pérez-Victoria JM. Heme synthesis through the life cycle of the heme auxotrophic parasite Leishmania major. FASEB J 2019; 33:13367-13385. [PMID: 31553893 DOI: 10.1096/fj.201901274rr] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme is an essential molecule synthetized through a broadly conserved 8-step route that has been lost in trypanosomatid parasites. Interestingly, Leishmania reacquired by horizontal gene transfer from γ-proteobacteria the genes coding for the last 3 enzymes of the pathway. Here we show that intracellular amastigotes of Leishmania major can scavenge heme precursors from the host cell to fulfill their heme requirements, demonstrating the functionality of this partial pathway. To dissect its role throughout the L. major life cycle, the significance of L. major ferrochelatase (LmFeCH), the terminal enzyme of the route, was evaluated. LmFeCH expression in a heterologous system demonstrated its activity. Knockout promastigotes lacking lmfech were not able to use the ferrochelatase substrate protoporphyrin IX as a source of heme. In vivo infection of Phlebotomus perniciosus with knockout promastigotes shows that LmFeCH is not required for their development in the sandfly. In contrast, the replication of intracellular amastigotes was hampered in vitro by the deletion of lmfech. However, LmFeCH-/- parasites produced disease in a cutaneous leishmaniasis murine model in a similar way as control parasites. Therefore, although L. major can synthesize de novo heme from macrophage precursors, this activity is dispensable being an unsuited target for leishmaniasis treatment.-Orrego, L. M., Cabello-Donayre, M., Vargas, P., Martínez-García, M., Sánchez, C., Pineda-Molina, E., Jiménez, M., Molina, R., Pérez-Victoria, J. M. Heme synthesis through the life cycle of the heme auxotrophic parasite Leishmania major.
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Affiliation(s)
- Lina M Orrego
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
| | - María Cabello-Donayre
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
| | - Paola Vargas
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
| | - Marta Martínez-García
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
| | - Clara Sánchez
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
| | - Estela Pineda-Molina
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
| | - Maribel Jiménez
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ricardo Molina
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - José M Pérez-Victoria
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Parque Tecnológico de la Salud (PTS) Granada, Granada, Spain
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Cruz AK, Freitas-Castro F. Genome and transcriptome analyses of Leishmania spp.: opening Pandora's box. Curr Opin Microbiol 2019; 52:64-69. [PMID: 31212190 DOI: 10.1016/j.mib.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/13/2019] [Indexed: 01/07/2023]
Abstract
In the last 30 years, significant advances in genetic manipulation tools along with complete genome and transcriptome sequencing have advanced our understanding of the biology of Leishmania parasites and their interplay with the sand fly and mammalian hosts. High-throughput sequencing in association with CRISPR/Cas9 have prepared the ground for significant advances. Given the richness of the progress made over the last decade, in this article, we focused on the most recent contributions of genome-wide and transcriptome analyses of Leishmania spp., which permit the comparison of life cycle stages, the evaluation of different strains and species in their natural niches and in the field and the simultaneously comparison of the gene expression profiles of parasites and hosts.
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Affiliation(s)
- Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Felipe Freitas-Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Rastrojo A, Corvo L, Lombraña R, Solana JC, Aguado B, Requena JM. Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major. Sci Rep 2019; 9:6919. [PMID: 31061406 PMCID: PMC6502937 DOI: 10.1038/s41598-019-43354-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 04/23/2019] [Indexed: 12/03/2022] Open
Abstract
Besides their medical relevance, Leishmania is an adequate model for studying post-transcriptional mechanisms of gene expression. In this microorganism, mRNA degradation/stabilization mechanisms together with translational control and post-translational modifications of proteins are the major drivers of gene expression. Leishmania parasites develop as promastigotes in sandflies and as amastigotes in mammalians, and during host transmission, the parasite experiences a sudden temperature increase. Here, changes in the transcriptome of Leishmania major promastigotes after a moderate heat shock were analysed by RNA-seq. Several of the up-regulated transcripts code for heat shock proteins, other for proteins previously reported to be amastigote-specific and many for hypothetical proteins. Many of the transcripts experiencing a decrease in their steady-state levels code for transporters, proteins involved in RNA metabolism or translational factors. In addition, putative long noncoding RNAs were identified among the differentially expressed transcripts. Finally, temperature-dependent changes in the selection of the spliced leader addition sites were inferred from the RNA-seq data, and particular cases were further validated by RT-PCR and Northern blotting. This study provides new insights into the post-transcriptional mechanisms by which Leishmania modulate gene expression.
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Affiliation(s)
- Alberto Rastrojo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura Corvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rodrigo Lombraña
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose C Solana
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Begoña Aguado
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Jose M Requena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, Madrid, Spain.
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Basmaciyan L, Robinson DR, Azas N, Casanova M. (De)glutamylation and cell death in Leishmania parasites. PLoS Negl Trop Dis 2019; 13:e0007264. [PMID: 31017892 PMCID: PMC6502457 DOI: 10.1371/journal.pntd.0007264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 05/06/2019] [Accepted: 02/26/2019] [Indexed: 11/18/2022] Open
Abstract
Trypanosomatids are flagellated protozoan parasites that are very unusual in terms of cytoskeleton organization but also in terms of cell death. Most of the Trypanosomatid cytoskeleton consists of microtubules, forming different substructures including a subpellicular corset. Oddly, the actin network appears structurally and functionally different from other eukaryotic actins. And Trypanosomatids have an apoptotic phenotype under cell death conditions, but the pathways involved are devoid of key mammal proteins such as caspases or death receptors, and the triggers involved in apoptotic induction remain unknown. In this article, we have studied the role of the post-translational modifications, deglutamylation and polyglutamylation, in Leishmania. We have shown that Leishmania apoptosis was linked to polyglutamylation and hypothesized that the cell survival process autophagy was linked to deglutamylation. A balance seems to be established between polyglutamylation and deglutamylation, with imbalance inducing microtubule or other protein modifications characterizing either cell death if polyglutamylation was prioritized, or the cell survival process of autophagy if deglutamylation was prioritized. This emphasizes the role of post-translational modifications in cell biology, inducing cell death or cell survival of infectious agents. Leishmania are unique unicellular organisms in terms of cytoskeleton organization and mechanisms of cell death. For example, the major cytoskeletal components of these parasites are microtubules, which form a subpellicular corset. In terms of cell death, an apoptotic phenotype has been characterized in Leishmania but the pathways remain unknown, being devoid of key mammal cell death proteins. In a previous article, we demonstrated that the cytoskeleton of this parasite is extensively glutamylated but, paradoxically, overexpression or inhibition of polyglutamylase expression have limited visible cellular consequences. In this manuscript, we have highlighted the link between polyglutamylation and Leishmania cell death, suggesting the importance of the polyglutamylation/deglutamylation balance in this parasite. Further, we have identified, for the first time in Leishmania, deglutamylases, among which one that, in an original manner, deglutamylates glutamates at branching points but also long glutamate side chains. This work emphasizes the role of post-translational modifications as essential regulators of protein function, not only of mammal cells such as neurons or ciliated/flagellated cells, but also of infectious agents. This work suggests an important and discernible “live or die”—“cell death or autophagy” balance pathway and the conceptual mechanism that is involved in cellular decision making.
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Affiliation(s)
- Louise Basmaciyan
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | - Nadine Azas
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Magali Casanova
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- * E-mail:
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25
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Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation. Sci Rep 2019; 9:6127. [PMID: 30992521 PMCID: PMC6467909 DOI: 10.1038/s41598-019-42511-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L. donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis-splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.
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Kariyawasam R, Mukkala AN, Lau R, Valencia BM, Llanos-Cuentas A, Boggild AK. Virulence factor RNA transcript expression in the Leishmania Viannia subgenus: influence of species, isolate source, and Leishmania RNA virus-1. Trop Med Health 2019; 47:25. [PMID: 31007536 PMCID: PMC6458769 DOI: 10.1186/s41182-019-0153-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Leishmania RNA virus-1 (LRV1) is a double-stranded RNA virus identified in 20-25% of Viannia-species endemic to Latin America, and is believed to accelerate cutaneous to mucosal leishmaniasis over time. Our objective was to quantify known virulence factor (VF) RNA transcript expression according to LRV1 status, causative species, and isolate source. METHODS Eight cultured isolates of Leishmania were used, four of which were LRV1-positive (Leishmania Viannia braziliensis [n = 1], L. (V.) guyanensis [n = 1], L. (V.) panamensis [n = 2]), and four were LRV1-negative (L. (V.) panamensis [n = 3], L. (V.) braziliensis [n = 1]). Promastigotes were inoculated into macrophage cultures, and harvested at 24 and 48 h. RNA transcript expression of hsp23, hsp70, hsp90, hsp100, mpi, cpb, and gp63 were quantified by qPCR. RESULTS RNA transcript expression of hsp100 (p = 0.012), cpb (p = 0.016), and mpi (p = 0.022) showed significant increases from baseline pure culture expression to 24- and 48-h post-macrophage infection, whereas hsp70 (p = 0.004) was significantly decreased. A trend toward increased transcript expression of hsp100 at baseline in isolates of L. (V.) panamensis was noted. Pooled VF RNA transcript expression by L. (V.) panamensis isolates was lower than that of L. (V.) braziliensis and L. (V.) guyananesis at 24 h (p = 0.03). VF RNA transcript expression did not differ by LRV1 status, or source of cultured isolate at baseline, 24, or 48 h; however, a trend toward increased VF RNA transcript expression of 2.71- and 1.93-fold change of mpi (p = 0.11) and hsp90 (p = 0.11), respectively, in LRV1 negative isolates was noted. Similarly, a trend toward lower levels of overall VF RNA transcript expression in clinical isolates (1.15-fold change) compared to ATCC® strains at 24 h was noted (p = 0.07). CONCLUSIONS Our findings suggest that known VF RNA transcript expression may be affected by the process of macrophage infection. We were unable to demonstrate definitively that LRV-1 presence affected VF RNA transcript expression in the species and isolates studied. L. (V.) guyanensis and L. (V.) braziliensis demonstrated higher pooled VF RNA transcript expression than L. (V.) panamensis; however, further analyses of protein expression to corroborate this finding are warranted.
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Affiliation(s)
| | - Avinash N. Mukkala
- Institute of Medical Sciences, University of Toronto, Toronto, ON Canada
| | - Rachel Lau
- Public Health Ontario Laboratory, Toronto, ON Canada
| | - Braulio M. Valencia
- Instituto de Medicina Tropical “Alejandro von Humboldt”, Lima, Peru
- Viral Immunology Systems Program, Kirby Institute, University of New South Wales, Sydney, Australia
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical “Alejandro von Humboldt”, Lima, Peru
- Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andrea K. Boggild
- Institute of Medical Sciences, University of Toronto, Toronto, ON Canada
- Public Health Ontario Laboratory, Toronto, ON Canada
- Department of Medicine, University of Toronto, Toronto, ON Canada
- Tropical Disease Unit, Toronto General Hospital, 200 Elizabeth Street, 13EN-218, Toronto, ON M5G 2C4 Canada
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Ruy PDC, Monteiro-Teles NM, Miserani Magalhães RD, Freitas-Castro F, Dias L, Aquino Defina TP, Rosas De Vasconcelos EJ, Myler PJ, Kaysel Cruz A. Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages. RNA Biol 2019; 16:639-660. [PMID: 30689499 DOI: 10.1080/15476286.2019.1574161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Leishmaniasis is a worldwide public health problem caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the most important species responsible for tegumentary leishmaniases in Brazil. An understanding of the molecular mechanisms underlying the success of this parasite is urgently needed. An in-depth study on the modulation of gene expression across the life cycle stages of L. braziliensis covering coding and noncoding RNAs (ncRNAs) was missing and is presented herein. Analyses of differentially expressed (DE) genes revealed that most prominent differences were observed between the transcriptomes of insect and mammalian proliferative forms (6,576 genes). Gene ontology (GO) analysis indicated stage-specific enriched biological processes. A computational pipeline and 5 ncRNA predictors allowed the identification of 11,372 putative ncRNAs. Most of the DE ncRNAs were found between the transcriptomes of insect and mammalian proliferative stages (38%). Of the DE ncRNAs, 295 were DE in all three stages and displayed a wide range of lengths, chromosomal distributions and locations; many of them had a distinct expression profile compared to that of their protein-coding neighbors. Thirty-five putative ncRNAs were submitted to northern blotting analysis, and one or more hybridization-positive signals were observed in 22 of these ncRNAs. This work presents an overview of the L. braziliensis transcriptome and its adjustments throughout development. In addition to determining the general features of the transcriptome at each life stage and the profile of protein-coding transcripts, we identified and characterized a variety of noncoding transcripts. The novel putative ncRNAs uncovered in L. braziliensis might be regulatory elements to be further investigated.
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Affiliation(s)
- Patrícia De Cássia Ruy
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Natália Melquie Monteiro-Teles
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Rubens Daniel Miserani Magalhães
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Felipe Freitas-Castro
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Leandro Dias
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Tania Paula Aquino Defina
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | | | - Peter J Myler
- b Center for Infectious Disease Research , Seattle, Washington , USA
| | - Angela Kaysel Cruz
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
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An Insight into the Constitutive Proteome Throughout Leishmania donovani Promastigote Growth and Differentiation. Int Microbiol 2018; 22:143-154. [DOI: 10.1007/s10123-018-00036-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/28/2023]
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Evolutionary Perspectives of Genotype-Phenotype Factors in Leishmania Metabolism. J Mol Evol 2018; 86:443-456. [PMID: 30022295 DOI: 10.1007/s00239-018-9857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
The sandfly midgut and the human macrophage phagolysosome provide antagonistic metabolic niches for the endoparasite Leishmania to survive and populate. Although these environments fluctuate across developmental stages, the relative changes in both these environments across parasite generations might remain gradual. Such environmental restrictions might endow parasite metabolism with a choice of specific genotypic and phenotypic factors that can constrain enzyme evolution for successful adaptation to the host. With respect to the available cellular information for Leishmania species, for the first time, we measure the relative contribution of eight inter-correlated predictors related to codon usage, GC content, gene expression, gene length, multi-functionality, and flux-coupling potential of an enzyme on the evolutionary rates of singleton metabolic genes and further compare their effects across three Leishmania species. Our analysis reveals that codon adaptation, multi-functionality, and flux-coupling potential of an enzyme are independent contributors of enzyme evolutionary rates, which can together explain a large variation in enzyme evolutionary rates across species. We also hypothesize that a species-specific occurrence of duplicated genes in novel subcellular locations can create new flux routes through certain singleton flux-coupled enzymes, thereby constraining their evolution. A cross-species comparison revealed both common and species-specific genes whose evolutionary divergence was constrained by multiple independent factors. Out of these, previously known pharmacological targets and virulence factors in Leishmania were identified, suggesting their evolutionary reasons for being important survival factors to the parasite. All these results provide a fundamental understanding of the factors underlying adaptive strategies of the parasite, which can be further targeted.
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Chen LF, Han XL, Li FX, Yao YY, Fang JP, Liu XJ, Li XC, Wu K, Liu M, Chen XG. Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing. Parasit Vectors 2018; 11:402. [PMID: 29996885 PMCID: PMC6042387 DOI: 10.1186/s13071-018-2983-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/27/2018] [Indexed: 11/19/2022] Open
Abstract
Background Toxoplasma gondii is one of the most important apicomplexan parasites and infects one-third of the human population worldwide. Transformation between the tachyzoite and bradyzoite stages in the intermediate host is central to chronic infection and life-long risk. There have been some transcriptome studies on T. gondii; however, we are still early in our understanding of the kinds and levels of gene expression that occur during the conversion between stages. Results We used high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo strategies. The expression-level analysis of 6996 T. gondii genes showed that over half (3986) were significantly differentially expressed during stage conversion, whereas 2205 genes were upregulated, and 1778 genes were downregulated in tachyzoites compared with bradyzoites. Several important gene families were expressed at relatively high levels. Comprehensive functional annotation and gene ontology analysis revealed that stress response-related genes are important for survival of bradyzoites in immune-competent hosts. We compared Trinity-based de novo and genome-based strategies, and found that the de novo assembly strategy compensated for the defects of the genome-based strategy by filtering out several transcripts with low expression or those unannotated on the genome. We also found some inaccuracies in the ToxoDB gene models. In addition, our analysis revealed that alternative splicing can be differentially regulated in response to life-cycle change. In depth analysis revealed a 20-nt, AG-rich sequence, alternative splicing locus from alt_acceptor motif search in tachyzoite. Conclusion This study represents the first large-scale effort to sequence the transcriptome of bradyzoites from T. gondii tissue cysts. Our data provide a comparative view of the tachyzoite and bradyzoite transcriptomes to allow a more complete dissection of all the molecular regulation mechanisms during stage conversions. A better understanding of the processes regulating stage conversion may guide targeted interventions to disrupt the transmission of T. gondii. Electronic supplementary material The online version of this article (10.1186/s13071-018-2983-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Long-Fei Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Xiao-Long Han
- Department of Bioinformatics, School of Basic Medicine School of Basic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Fen-Xiang Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Yun-Ying Yao
- Epidemiology and Infection Control Branch, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, 518106, Guangdong, China
| | - Jin-Ping Fang
- First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiao-Ju Liu
- First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiao-Cong Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Kun Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Min Liu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
| | - Xiao-Guang Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
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Abstract
Extracellular vesicles (EVs) are released by a wide number of cells including blood cells, immune system cells, tumour cells, adult and embryonic stem cells. EVs are a heterogeneous group of vesicles (~30-1000 nm) including microvesicles and exosomes. The physiological release of EVs represents a normal state of the cell, raising a metabolic equilibrium between catabolic and anabolic processes. Moreover, when the cells are submitted to stress with different inducers or in pathological situations (malignancies, chronic diseases, infectious diseases.), they respond with an intense and dynamic release of EVs. The EVs released from stimulated cells vs those that are released constitutively may themselves differ, both physically and in their cargo. EVs contain protein, lipids, nucleic acids and biomolecules that can alter cell phenotypes or modulate neighbouring cells. In this review, we have summarized findings involving EVs in certain protozoan diseases. We have commented on strategies to study the communicative roles of EVs during host-pathogen interaction and hypothesized on the use of EVs for diagnostic, preventative and therapeutic purposes in infectious diseases. This kind of communication could modulate the innate immune system and reformulate concepts in parasitism. Moreover, the information provided within EVs could produce alternatives in translational medicine.
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Rastrojo A, García-Hernández R, Vargas P, Camacho E, Corvo L, Imamura H, Dujardin JC, Castanys S, Aguado B, Gamarro F, Requena JM. Genomic and transcriptomic alterations in Leishmania donovani lines experimentally resistant to antileishmanial drugs. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:246-264. [PMID: 29689531 PMCID: PMC6039315 DOI: 10.1016/j.ijpddr.2018.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/10/2018] [Accepted: 04/10/2018] [Indexed: 12/20/2022]
Abstract
Leishmaniasis is a serious medical issue in many countries around the World, but it remains largely neglected in terms of research investment for developing new control and treatment measures. No vaccines exist for human use, and the chemotherapeutic agents currently used are scanty. Furthermore, for some drugs, resistance and treatment failure are increasing to alarming levels. The aim of this work was to identify genomic and trancriptomic alterations associated with experimental resistance against the common drugs used against VL: trivalent antimony (SbIII, S line), amphotericin B (AmB, A line), miltefosine (MIL, M line) and paromomycin (PMM, P line). A total of 1006 differentially expressed transcripts were identified in the S line, 379 in the A line, 146 in the M line, and 129 in the P line. Also, changes in ploidy of chromosomes and amplification/deletion of particular regions were observed in the resistant lines regarding the parental one. A series of genes were identified as possible drivers of the resistance phenotype and were validated in both promastigotes and amastigotes from Leishmania donovani, Leishmania infantum and Leishmania major species. Remarkably, a deletion of the gene LinJ.36.2510 (coding for 24-sterol methyltransferase, SMT) was found to be associated with AmB-resistance in the A line. In the P line, a dramatic overexpression of the transcripts LinJ.27.T1940 and LinJ.27.T1950 that results from a massive amplification of the collinear genes was suggested as one of the mechanisms of PMM resistance. This conclusion was reinforced after transfection experiments in which significant PMM-resistance was generated in WT parasites over-expressing either gene LinJ.27.1940 (coding for a D-lactate dehydrogenase-like protein, D-LDH) or gene LinJ.27.1950 (coding for an aminotransferase of branched-chain amino acids, BCAT). This work allowed to identify new drivers, like SMT, the deletion of which being associated with resistance to AmB, and the tandem D-LDH-BCAT, the amplification of which being related to PMM resistance.
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Affiliation(s)
- Alberto Rastrojo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Paola Vargas
- Instituto de Parasitología y Biomedicina ''López-Neyra'' (IPBLN-CSIC), Granada, Spain
| | - Esther Camacho
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura Corvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Santiago Castanys
- Instituto de Parasitología y Biomedicina ''López-Neyra'' (IPBLN-CSIC), Granada, Spain
| | - Begoña Aguado
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Gamarro
- Instituto de Parasitología y Biomedicina ''López-Neyra'' (IPBLN-CSIC), Granada, Spain.
| | - Jose M Requena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
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El-Ashram S, Li C, Abouhajer F, Mehmood R, Al Nasr I, Zhang Y, Lu T, Yili D, Suo X, Haoji Z, Li Z, Huang S. An ex vivo abomasal ovine model to study the immediate immune response in the context of Haemonchus contortus larval-stage. Vet Parasitol 2018; 254:105-113. [PMID: 29656994 DOI: 10.1016/j.vetpar.2018.02.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/22/2018] [Accepted: 02/28/2018] [Indexed: 12/11/2022]
Abstract
We have set up an ex vivo ovine abomasal model, which can mimic the multicellular process to explore the early steps in haemonchine nematode infection using RNA-seq technology. Ovine abomasal explants were collected for histological and transcriptional analysis and supernatants collected to quantitate lactate dehydrogenase (LDH) enzymes. Atotal of 233 were substantially induced genes between L4-inoculated and uninoculated-control tissues, respectively. However, a total of 14 were considerably down-regulated genes between the 51 aforementioned tissues. Fifteen pathways were annotated by Kyoto Encyclopedia of Genes, and Genomes pathway analysis accounted for the significant percentage in immediate response to larval-stage of H. contortus. Key genes upregulated in response to the addition of L4-inoculum of H. contortus were IL-6, IL-8, C1q, Atypical chemokine receptor-3, chemokine ligand-2, manganese superoxide dismutase, integrin alpha-7, -8, -9, integrin subunit beta-1, integrin subunit beta 6, intercellular adhesion molecule-1 and actin alpha-1. This study shows for the first time that galectin-1 is up-regulated in an ex vivo abomasal segment model exposed to L4-inoculum of H. contortus following 6 h of incubation. The abomasal segment model has been shown to be a suitable tool to study the haemonchine larval-stage effects on the ovine abomasal tissues prior to in vivo assessment.
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Affiliation(s)
- Saeed El-Ashram
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China; State Key Laboratory for Agrobiotechnology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Faculty of Science, Kafr ElSheikh University, Kafr ElSheikh, Egypt.
| | - Cuiping Li
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Fathi Abouhajer
- Faculty of Education, Asmarya University for Islamic Sciences, Zliten, Libya
| | - Rashid Mehmood
- Department of Computer Science and Information Technology, University of Kotli, AJ&K Pakistan
| | - Ibrahim Al Nasr
- College of Science and Arts in Unaizah, Qassim University, Unaizah, Saudi Arabia; College of Applied Health Sciences in Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Yinghui Zhang
- School of Food Science and Engineering, Foshan University (Northern Campus), Shishan, Naihai district of Foshan City, Guangdong Province 528231, China
| | - Tang Lu
- School of Food Science and Engineering, Foshan University (Northern Campus), Shishan, Naihai district of Foshan City, Guangdong Province 528231, China
| | - Ding Yili
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Xun Suo
- State Key Laboratory for Agrobiotechnology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhang Haoji
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Zhili Li
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China
| | - Shujian Huang
- College of Life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan 528231, Guangdong Province, China.
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Abouhajer F, El-Ashram S, Karama M, Huang S, Liu JF. An ex vivo ruminal ovine model to study the immediate immune response in the context of bacterial lipopolysaccharide. Funct Integr Genomics 2018; 18:277-285. [PMID: 29429072 DOI: 10.1007/s10142-018-0589-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/29/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
Abstract
We have set up an ex vivo ovine ruminal model, which can mimic the multicellular process to explore the early steps in Salmonella typhimurium lipopolysaccharide (LPS) stimulation using RNA-seq technology. Ovine ruminal explants were collected for histological and transcriptional analysis and supernatants collected to quantitate lactate dehydrogenase (LDH) enzymes. A total of 8 and 523 genes were significantly over-expressed between LPS-treated and control tissues at 6 and 12 h, respectively. However, six and seven hundred and thirteen genes were substantially repressed between the aforementioned tissues, correspondingly. Key genes up-regulated in response to the addition of LPS were tumor necrosis factor (TNF), interlukin (IL)-1 beta(b), IL-6, IL-8, IL-17B, IL-19, MMP-1, MMP-3, and integrin alpha 2 (ITGA8, 9). This study shows for the first time that galectin-1 is up-regulated in an ex vivo ruminal segment model exposed to bacterial lipopolysaccharide following 6 h of incubation. The ruminal segment model has been shown to be a suitable tool to study the bacterial lipopolysaccharide effects on the ovine ruminal tissues prior to in vivo assessment.
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Affiliation(s)
- Fathi Abouhajer
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Faculty of Education, Asmarya University for Islamic Sciences, Zliten, Libya
| | - Saeed El-Ashram
- College of life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, Guangdong, 528231, China.
- Faculty of Science, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt.
| | - Musafiri Karama
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Shujian Huang
- College of life Science and Engineering, Foshan University, 18 Jiangwan Street, Foshan, Guangdong, 528231, China
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Aoki JI, Muxel SM, Zampieri RA, Laranjeira-Silva MF, Müller KE, Nerland AH, Floeter-Winter LM. RNA-seq transcriptional profiling of Leishmania amazonensis reveals an arginase-dependent gene expression regulation. PLoS Negl Trop Dis 2017; 11:e0006026. [PMID: 29077741 PMCID: PMC5678721 DOI: 10.1371/journal.pntd.0006026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/08/2017] [Accepted: 10/10/2017] [Indexed: 01/01/2023] Open
Abstract
Background Leishmania is a protozoan parasite that alternates its life cycle between the sand-fly vector and the mammalian host. This alternation involves environmental changes and leads the parasite to dynamic modifications in morphology, metabolism, cellular signaling and regulation of gene expression to allow for a rapid adaptation to new conditions. The L-arginine pathway in L. amazonensis is important during the parasite life cycle and interferes in the establishment and maintenance of the infection in mammalian macrophages. Host arginase is an immune-regulatory enzyme that can reduce the production of nitric oxide by activated macrophages, directing the availability of L-arginine to the polyamine pathway, resulting in parasite replication. In this work, we performed transcriptional profiling to identify differentially expressed genes in L. amazonensis wild-type (La-WT) versus L. amazonensis arginase knockout (La-arg-) promastigotes and axenic amastigotes. Methodology/Principal findings A total of 8253 transcripts were identified in La-WT and La-arg- promastigotes and axenic amastigotes, about 60% of them codifying hypothetical proteins and 443 novel transcripts, which did not match any previously annotated genes. Our RNA-seq data revealed that 85% of genes were constitutively expressed. The comparison of transcriptome and metabolome data showed lower levels of arginase and higher levels of glutamate-5-kinase in La-WT axenic amastigotes compared to promastigotes. The absence of arginase activity in promastigotes increased the levels of pyrroline 5-carboxylate reductase, but decreased the levels of arginosuccinate synthase, pyrroline 5-carboxylate dehydrogenase, acetylornithine deacetylase and spermidine synthase transcripts levels. These observations can explain previous metabolomic data pointing to the increase of L-arginine, citrulline and L-glutamate and reduction of aspartate, proline, ornithine and putrescine. Altogether, these results indicate that arginase activity is important in Leishmania gene expression modulation during differentiation and adaptation to environmental changes. Here, we confirmed this hypothesis with the identification of differential gene expression of the enzymes involved in biosynthesis of amino acids, arginine and proline metabolism and arginine biosynthesis. Conclusions/Significance All data provided information about the transcriptomic profiling and the expression levels of La-WT and La-arg- promastigotes and axenic amastigotes. These findings revealed the importance of arginase in parasite survival and differentiation, and indicated the existence of a coordinated response in the absence of arginase activity related to arginine and polyamine pathways. Leishmania are auxotrophic for many essential nutrients, including amino acids. In this way, the parasite needs to uptake the amino acids from the environment. The uptake of amino acids is mediated by amino acid transporters that are unique for Leishmania. As part of polyamine pathway, the arginase converts L-arginine to ornithine and furthermore to putrescine, products which are essential for parasite growth. On the other hand, the absence of arginase activity could alter the metabolism of the parasite to surpass the external signals during the life cycle and the fate of infection. The transcriptional profiling of La-WT and La-arg- promastigotes and axenic amastigotes revealed 8253 transcripts, 60% encoding hypothetical proteins and 443 novel transcripts. In addition, our data revealed that 85% of the genes were constitutively expressed. Among the 15% (1268 genes) of the differentially expressed genes, we identified genes up- and down-regulated comparing the transcript abundance from different life cycle stages of the parasite and in the presence or absence of arginase. We also combined the transcriptional with metabolic profile that revealed a proportional correlation between enzyme and metabolites in the polyamine pathway. The differentiation of promastigotes to amastigotes alters the expression of enzymes from polyamines biosynthesis, which modulates ornithine, L-glutamate, proline and putrescine levels. In addition, the absence of arginase activity increased the levels of L-arginine, citrulline and L-glutamate and decreased the levels of aspartate, proline, ornithine and putrescine in promastigotes by differential modulation of genes involved in its metabolism. Altogether these data provided additional insights into how Leishmania is able to modulate its biological functions in the presence or absence of arginase activity to survive during environmental changes.
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Affiliation(s)
- Juliana Ide Aoki
- Department of Physiology, Institute of Bioscience, University of Sao Paulo, Sao Paulo, Brazil
- * E-mail: (JIA); (LMFW)
| | - Sandra Marcia Muxel
- Department of Physiology, Institute of Bioscience, University of Sao Paulo, Sao Paulo, Brazil
| | | | | | - Karl Erik Müller
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Lucile Maria Floeter-Winter
- Department of Physiology, Institute of Bioscience, University of Sao Paulo, Sao Paulo, Brazil
- * E-mail: (JIA); (LMFW)
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Cuypers B, Domagalska MA, Meysman P, Muylder GD, Vanaerschot M, Imamura H, Dumetz F, Verdonckt TW, Myler PJ, Ramasamy G, Laukens K, Dujardin JC. Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids. Sci Rep 2017. [PMID: 28623350 PMCID: PMC5473914 DOI: 10.1038/s41598-017-03987-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
High throughput sequencing techniques are poorly adapted for in vivo studies of parasites, which require prior in vitro culturing and purification. Trypanosomatids, a group of kinetoplastid protozoans, possess a distinctive feature in their transcriptional mechanism whereby a specific Spliced Leader (SL) sequence is added to the 5'end of each mRNA by trans-splicing. This allows to discriminate Trypansomatid RNA from mammalian RNA and forms the basis of our new multiplexed protocol for high-throughput, selective RNA-sequencing called SL-seq. We provided a proof-of-concept of SL-seq in Leishmania donovani, the main causative agent of visceral leishmaniasis in humans, and successfully applied the method to sequence Leishmania mRNA directly from infected macrophages and from highly diluted mixes with human RNA. mRNA profiles obtained with SL-seq corresponded largely to those obtained from conventional poly-A tail purification methods, indicating both enumerate the same mRNA pool. However, SL-seq offers additional advantages, including lower sequencing depth requirements, fast and simple library prep and high resolution splice site detection. SL-seq is therefore ideal for fast and massive parallel sequencing of parasite transcriptomes directly from host tissues. Since SLs are also present in Nematodes, Cnidaria and primitive chordates, this method could also have high potential for transcriptomics studies in other organisms.
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Affiliation(s)
- Bart Cuypers
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Advanced Database Research and Modeling group (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Malgorzata A Domagalska
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Meysman
- Advanced Database Research and Modeling group (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Géraldine de Muylder
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Manu Vanaerschot
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Fidock Lab, Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Hideo Imamura
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Franck Dumetz
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Thomas Wolf Verdonckt
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Peter J Myler
- Center for Infectious Disease Research, Seattle, Washington, United States of America.,Department of Global Health and Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, Washington, United States of America
| | - Gowthaman Ramasamy
- Center for Infectious Disease Research, Seattle, Washington, United States of America
| | - Kris Laukens
- Advanced Database Research and Modeling group (ADReM), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Early and late gene expression profiles of the ovine mucosa in response to Haemonchus contortus infection employing Illumina RNA-seq technology. Parasitol Int 2017; 66:681-692. [PMID: 28552633 DOI: 10.1016/j.parint.2017.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/03/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023]
Abstract
We conducted herein transcriptome sequencing of the ovine abomasal tissues using the Illumina HiSeq 4000 platform to segregate early and late H. contortus-infected sheep (7 and 50days post-infected groups, respectively) from the control naive ones. A total of 548, 357 and 7 were substantially induced genes in 7days post-infection versus uninfected-control group, 50days post-infection versus 7days post-infection (7dpi), and 50days post-infection (50dpi) versus uninfected-control group, respectively. However, a total of 301, 355 and 11 were significantly repressed genes between 7dpi versus uninfected-control group, 50dpi versus 7dpi, and 50dpi versus uninfected-control group, correspondingly. This indicates that H. contortus infection induced a more potent activation of abomasal gene expression in the early stage of infection as compared to the late stage. Seven pathways were annotated by Kyoto Encyclopedia of Genes, and Genomes pathway analysis accounted for the significant percentage in early H. contortus infection. This study shows for the first time that both galectin-11 and matricellular protein osteopontin are up-regulated in abomasal tissue after chronic H. contortus infection, while galectin-4 is specifically down-regulated in the early infection. Additionally, our results showed that the induction or repression of these molecules is likely to determine the infection progression.
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Freitas Castro F, Ruy PC, Nogueira Zeviani K, Freitas Santos R, Simões Toledo J, Kaysel Cruz A. Evidence of putative non-coding RNAs from Leishmania untranslated regions. Mol Biochem Parasitol 2017; 214:69-74. [PMID: 28385563 DOI: 10.1016/j.molbiopara.2017.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/28/2022]
Abstract
Non-coding RNAs (ncRNAs) are regulatory elements present in a wide range of organisms, including trypanosomatids. ncRNAs transcribed from the untranslated regions (UTRs) of coding genes have been described in the transcriptomes of several eukaryotes, including Trypanosoma brucei. To uncover novel putative ncRNAs in two Leishmania species, we examined a L. major cDNA library and a L. donovani non-polysomal RNA library. Using a combination of computational analysis and experimental approaches, we classified 26 putative ncRNA in L. major, of these, 5 arising from intergenic regions and 21 from untranslated regions. In L. donovani, we classified 37 putative ncRNAs, of these, 7 arising from intergenic regions, and 30 from UTRs. Our results suggest, for the first time, that UTR-transcripts may be a common feature in the eukaryote Leishmania similarly to those previously shown in T. brucei and other eukaryotes.
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Affiliation(s)
- Felipe Freitas Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Patricia C Ruy
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Karina Nogueira Zeviani
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Ramon Freitas Santos
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Juliano Simões Toledo
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil.
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Untranslated regions of mRNA and their role in regulation of gene expression in protozoan parasites. J Biosci 2017; 42:189-207. [PMID: 28229978 DOI: 10.1007/s12038-016-9660-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protozoan parasites are one of the oldest living entities in this world that throughout their existence have shown excellent resilience to the odds of survival and have adapted beautifully to ever changing rigors of the environment. In view of the dynamic environment encountered by them throughout their life cycle, and in establishing pathogenesis, it is unsurprising that modulation of gene expression plays a fundamental role in their survival. In higher eukaryotes, untranslated regions (UTRs) of transcripts are one of the crucial regulators of gene expression (influencing mRNA stability and translation efficiency). Parasitic protozoan genome studies have led to the characterization (in silico, in vitro and in vivo) of a large number of their genes. Comparison of higher eukaryotic UTRs with parasitic protozoan UTRs reveals the existence of several similar and dissimilar facets of the UTRs. This review focuses on the elements of UTRs of medically important protozoan parasites and their regulatory role in gene expression. Such information may be useful to researchers in designing gene targeting strategies linked with perturbation of host-parasite relationships leading to control of specific parasites.
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A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major. Acta Trop 2017; 167:21-25. [PMID: 27988178 DOI: 10.1016/j.actatropica.2016.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/03/2016] [Accepted: 12/12/2016] [Indexed: 01/07/2023]
Abstract
Cutaneous leishmaniasis (CL) is caused by a kinetoplastid protozoan parasite Leishmania major, as a skin ulcer at the site of the sandfly bite. CL is curable and in most cases ulcers heal spontaneously within three to six months leaving a scar and disfiguration. Complete genome of L. major was reported in 2005 at the very initial phase of kinetoplastid parasite genome sequencing project. Presently, L. major genome is most studied and comprehensively annotated genome and therefore, it is being used as a reference genome for annotating recently sequenced Leishmanial genomes. A recent study reporting global transcriptome of L. major promastigotes, identified 1884 uniquely expressed non-coding RNAs (ncRNA) in L. major. In the current study, an in-depth analysis of the 1884 novel ncRNAs was carried out using a proteogenomic approach to identify their protein coding potential. Our analysis resulted in identification of eight novel protein coding genes based on mass spectrometry data. We have analyzed each of these eight novel CDS and in the process have improved the genome annotation of L. major on the basis of mass spectrometry derived peptide data. Although sequenced a decade ago, the improvement in the L. major genome annotation thus is an ongoing process.
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Patino LH, Ramírez JD. RNA-seq in kinetoplastids: A powerful tool for the understanding of the biology and host-pathogen interactions. INFECTION GENETICS AND EVOLUTION 2017; 49:273-282. [PMID: 28179142 DOI: 10.1016/j.meegid.2017.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 12/31/2022]
Abstract
The kinetoplastids include a large number of parasites responsible for serious diseases in humans and animals (Leishmania and Trypanosoma brucei) considered endemic in several regions of the world. These parasites are characterized by digenetic life cycles that undergo morphological and genetic changes that allow them to adapt to different microenvironments on their vertebrates and invertebrates hosts. Recent advances in ´omics´ technology, specifically transcriptomics have allowed to reveal aspects associated with such molecular changes. So far, different techniques have been used to evaluate the gene expression profile during the various stages of the life cycle of these parasites and during the host-parasite interactions. However, some of them have serious drawbacks that limit the precise study and full understanding of their transcriptomes. Therefore, recently has been implemented the latest technology (RNA-seq), which overcomes the drawbacks of traditional methods. In this review, studies that so far have used RNA-seq are presented and allowed to expand our knowledge regarding the biology of these parasites and their interactions with their hosts.
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Affiliation(s)
- Luz Helena Patino
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24# 63C-69, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24# 63C-69, Bogotá, Colombia.
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Requena JM, Rastrojo A, Garde E, López MC, Thomas MC, Aguado B. Dataset for distribution of SIDER2 elements in the Leishmania major genome and transcriptome. Data Brief 2017; 11:39-43. [PMID: 28127581 PMCID: PMC5247276 DOI: 10.1016/j.dib.2017.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 12/27/2016] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
This paper contains data related to the research article entitled “Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts” [1]. SIDER2 elements are repeated sequences, derived from, nowadays, extinct retrotransposons, that populate the genomes of protist of the genera Leishmania. This dataset (Supplementary file 1), an inventory of 1100 SIDER2 elements, was generated by surveying the L. major complete genome using bioinformatics tools with further manual refinements. In addition to the genomic distribution of these elements (summarized in Fig. 1), this dataset contains information regarding their association with specific transcripts, based on the recently established transcriptome for L. major[2].
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Affiliation(s)
- Jose M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Esther Garde
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Manuel C López
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), 18016 Granada, Spain
| | - M Carmen Thomas
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), 18016 Granada, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Torres F, Arias-Carrasco R, Caris-Maldonado JC, Barral A, Maracaja-Coutinho V, De Queiroz ATL. LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. Database (Oxford) 2017; 2017:3867745. [PMID: 29220437 PMCID: PMC5502370 DOI: 10.1093/database/bax047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 11/17/2022]
Abstract
Database URL www.leishdb.com.
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Affiliation(s)
- Felipe Torres
- Centro de Pesquisas Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
- Programa de Pós-Graduação em Computação Aplicada (PGCA), Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Raúl Arias-Carrasco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - José C. Caris-Maldonado
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Aldina Barral
- Centro de Pesquisas Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
- Universidade Federal da Bahia, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia (iii-INCT), São Paulo, Brazil
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Beagle Bioinformatics, Santiago, Chile
- Instituto Vandique, João Pessoa, Brazil
| | - Artur T. L. De Queiroz
- Centro de Pesquisas Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
- Programa de Pós-Graduação em Computação Aplicada (PGCA), Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
- Instituto Nacional de Ciência e Tecnologia de Investigação em Imunologia (iii-INCT), São Paulo, Brazil
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Requena JM, Rastrojo A, Garde E, López MC, Thomas MC, Aguado B. Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts. Mol Biochem Parasitol 2016; 212:9-15. [PMID: 28034676 DOI: 10.1016/j.molbiopara.2016.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 01/09/2023]
Abstract
The genomes of most eukaryotic organisms contain a large number of transposable elements that are able to move from one genomic site to another either by transferring of DNA mobile elements (transposons) or transpose via reverse transcription of an RNA intermediate (retroposons). An exception to this rule is found in protists of the subgenus Leishmania, in which active retroposons degenerated after a flourishing era, leaving only retroposon remains; these have been classified into two families: SIDER1 and SIDER2. In this work, we have re-examined the elements belonging to the family SIDER2 present in the genome of Leishmania major with the aim of providing a nomenclature that will facilitate a future reference to particular elements. According to sequence conservation, the 1100 SIDER2 elements have been grouped into subfamilies, and the inferred taxonomic relationships have also been incorporated into the nomenclature. Additionally, we are providing detailed data regarding the genomic distribution of these elements and their association with specific transcripts, based on the recently established transcriptome for L. major. Thus, the presented data can help to study and better understand the roles played by these degenerated retroposons in both regulation of gene expression and genome plasticity.
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Affiliation(s)
- Jose M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Esther Garde
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Manuel C López
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), 18016 Granada, Spain
| | - M Carmen Thomas
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), 18016 Granada, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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Penha LL, Hoffmann L, Souza SSD, Martins ACDA, Bottaro T, Prosdocimi F, Faffe DS, Motta MCM, Ürményi TP, Silva R. Symbiont modulates expression of specific gene categories in Angomonas deanei. Mem Inst Oswaldo Cruz 2016; 111:686-691. [PMID: 27706380 PMCID: PMC5125052 DOI: 10.1590/0074-02760160228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/10/2016] [Indexed: 11/21/2022] Open
Abstract
Trypanosomatids are parasites that cause disease in humans, animals, and plants. Most
are non-pathogenic and some harbor a symbiotic bacterium. Endosymbiosis is part of
the evolutionary process of vital cell functions such as respiration and
photosynthesis. Angomonas deanei is an example of a
symbiont-containing trypanosomatid. In this paper, we sought to investigate how
symbionts influence host cells by characterising and comparing the transcriptomes of
the symbiont-containing A. deanei (wild type) and the symbiont-free
aposymbiotic strains. The comparison revealed that the presence of the symbiont
modulates several differentially expressed genes. Empirical analysis of differential
gene expression showed that 216 of the 7625 modulated genes were significantly
changed. Finally, gene set enrichment analysis revealed that the largest categories
of genes that downregulated in the absence of the symbiont were those involved in
oxidation-reduction process, ATP hydrolysis coupled proton transport and glycolysis.
In contrast, among the upregulated gene categories were those involved in
proteolysis, microtubule-based movement, and cellular metabolic process. Our results
provide valuable information for dissecting the mechanism of endosymbiosis in
A. deanei.
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Affiliation(s)
- Luciana Loureiro Penha
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Luísa Hoffmann
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Silvanna Sant'Anna de Souza
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | | | - Thayane Bottaro
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Francisco Prosdocimi
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Débora Souza Faffe
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | | | - Turán Péter Ürményi
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Rosane Silva
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
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Lombraña R, Álvarez A, Fernández-Justel JM, Almeida R, Poza-Carrión C, Gomes F, Calzada A, Requena JM, Gómez M. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major. Cell Rep 2016; 16:1774-1786. [PMID: 27477279 DOI: 10.1016/j.celrep.2016.07.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/26/2016] [Accepted: 07/01/2016] [Indexed: 01/04/2023] Open
Abstract
Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs). Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance.
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Affiliation(s)
- Rodrigo Lombraña
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alba Álvarez
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José Miguel Fernández-Justel
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Almeida
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - César Poza-Carrión
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Fábia Gomes
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Arturo Calzada
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
| | - José María Requena
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - María Gómez
- Functional Organization of the Genome Group, Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
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Pratlong F, Balard Y, Lami P, Talignani L, Ravel C, Dereure J, Lefebvre M, Serres G, Bastien P, Dedet JP. The Montpellier Leishmania Collection, from a Laboratory Collection to a Biological Resource Center: A 39-Year-Long Story. Biopreserv Biobank 2016; 14:470-479. [PMID: 27379470 DOI: 10.1089/bio.2015.0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report the development of a laboratory collection of Leishmania that was initiated in 1975 and, after 39 years, has become an international Biological Resource Center (BRC-Leish, Montpellier, France, BioBank No. BB-0033-00052), which includes 6353 strains belonging to 36 Leishmania taxa. This is a retrospective analysis of the technical and organizational changes that have been adopted over time to take into account the technological advances and related modifications in the collection management and quality system. The technical improvements concerned the culture and cryopreservation techniques, strain identification by isoenzymatic and molecular techniques, data computerization and quality management to meet the changes in international standards, and in the cryogenic and microbiological safety procedures. The BRC is working toward obtaining the NF-S 96-900 certification in the coming years. Our long-term expertise in Leishmania storage and typing and collection maintenance should encourage field epidemiologists and clinical practitioners in endemic countries to secure their own strain collection with the help of the French BRC-Leish.
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Affiliation(s)
- Francine Pratlong
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Yves Balard
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Patrick Lami
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Loïc Talignani
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Christophe Ravel
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Jacques Dereure
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Michèle Lefebvre
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Ghislaine Serres
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Patrick Bastien
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
| | - Jean-Pierre Dedet
- Laboratory of Parasitology-Mycology, Faculty of Medicine, University of Montpellier-National Reference Centre for Leishmaniases-Unit MIVEGEC (CNRS 5290/IRD 224/University of Montpellier)-Academic Hospital Center (C.H.U.) of Montpellier , Montpellier, France
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Alcolea PJ, Alonso A, Domínguez M, Parro V, Jiménez M, Molina R, Larraga V. Influence of the Microenvironment in the Transcriptome of Leishmania infantum Promastigotes: Sand Fly versus Culture. PLoS Negl Trop Dis 2016; 10:e0004693. [PMID: 27163123 PMCID: PMC4862625 DOI: 10.1371/journal.pntd.0004693] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 04/14/2016] [Indexed: 01/04/2023] Open
Abstract
Zoonotic visceral leishmaniasis is a vector-borne disease caused by Leishmania infantum in the Mediterranean Basin, where domestic dogs and wild canids are the main reservoirs. The promastigote stage replicates and develops within the gut of blood-sucking phlebotomine sand flies. Mature promastigotes are injected in the dermis of the mammalian host and differentiate into the amastigote stage within parasitophorous vacuoles of phagocytic cells. The major vector of L. infantum in Spain is Phlebotomus perniciosus. Promastigotes are routinely axenized and cultured to mimic in vitro the conditions inside the insect gut, which allows for most molecular, cellular, immunological and therapeutical studies otherwise inviable. Culture passages are known to decrease infectivity, which is restored by passage through laboratory animals. The most appropriate source of promastigotes is the gut of the vector host but isolation of the parasite is technically challenging. In fact, this option is not viable unless small samples are sufficient for downstream applications like promastigote cultures and nucleic acid amplification. In this study, in vitro infectivity and differential gene expression have been studied in cultured promastigotes at the stationary phase and in promastigotes isolated from the stomodeal valve of the sand fly P. perniciosus. About 20 ng RNA per sample could be isolated. Each sample contained L. infantum promastigotes from 20 sand flies. RNA was successfully amplified and processed for shotgun genome microarray hybridization analysis. Most differentially regulated genes are involved in regulation of gene expression, intracellular signaling, amino acid metabolism and biosynthesis of surface molecules. Interestingly, meta-analysis by hierarchical clustering supports that up-regulation of 22.4% of the differentially regulated genes is specifically enhanced by the microenvironment (i.e. sand fly gut or culture). The correlation between cultured and naturally developed promastigotes is strong but not very high (Pearson coefficient R2 = 0.727). Therefore, the influence of promastigote culturing should be evaluated case-by-case in experimentation. The protozoan parasite Leishmania infantum causes visceral leishmaniasis in humans and is responsible for a recent outbreak reported in central Spain. Domestic dogs and wild canids are the main reservoirs. The life cycle of the parasite involves two stages and two hosts. The motile promastigote stage differentiates within the gut of the sand fly vector host and develops into non-motile amastigotes within phagocytes of the mammalian host. Promastigotes are routinely cultured in liquid media because it is assumed that they mimic the conditions within the gut of the insect. Therefore, the culture model is used in most studies about the biology of the parasite, pathogenesis and development of vaccines and new compounds for treatment. Isolating promastigotes from the natural microenvironment (i.e. the vector host) is desirable but technically challenging. We were able to perform a high-throughput analysis of gene expression thanks to mRNA amplification. The over-expressed genes detected may influence life cycle progression depending on the promastigote microenvironment (i.e. culture or vector host). Upcoming studies based on these results may reveal new therapeutic targets or vaccine candidates. Our results suggest that evaluating the influence of cultures in experimentation is convenient.
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Affiliation(s)
- Pedro J. Alcolea
- Laboratorio de Parasitología Molecular, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
| | - Ana Alonso
- Laboratorio de Parasitología Molecular, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mercedes Domínguez
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Víctor Parro
- Laboratorio de Ecología Molecular, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas”—Consejo Superior de Investigaciones Científicas, Torrejón de Ardoz, Madrid, Spain
| | - Maribel Jiménez
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ricardo Molina
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Vicente Larraga
- Laboratorio de Parasitología Molecular, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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50
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Alonso G, Rastrojo A, López-Pérez S, Requena JM, Aguado B. Resequencing and assembly of seven complex loci to improve the Leishmania major (Friedlin strain) reference genome. Parasit Vectors 2016; 9:74. [PMID: 26857920 PMCID: PMC4746890 DOI: 10.1186/s13071-016-1329-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/20/2016] [Indexed: 01/22/2023] Open
Abstract
Background Leishmania parasites cause severe human diseases known as leishmaniasis. These eukaryotic microorganisms possess an atypical chromosomal architecture and the regulation of gene expression occurs almost exclusively at post-transcriptional levels. Accordingly, sequencing of the genome of Leishmania major, and subsequently the genome of other related species, was paramount for highlighting these peculiar molecular aspects. Recently, we carried out an analysis of gene expression by massive sequencing of RNA in the L. major promastigote, and data derived from that analysis were suggestive of possible errors in the current genome assembly for this Leishmania species. Results During the analysis by RNA-Seq of the transcriptome for L. major Friedlin strain, 163,714 reads could not be aligned with the reference genome. Thus, de novo assembly with these reads was carried out and the resulting contigs were further analyzed. After detailed homology searches using available databases, it was postulated that 15 contigs might correspond to genomic sequences lost during the initial genome assembly of the L. major Friedlin strain. This was experimentally confirmed by PCR amplification, cloning and sequencing of the new genomic regions. As a result, we have identified seven regions of the L. major (Friedlin) genome that were lost during the sequence assembly. This led to the uncovering of six new genes (LmjF.15.1475, LmjF.15.0285, LmjF.24.0765, LmjF.14.0860, LmjF.19.0305, and LmjF.27.2035), and correction of the annotation for two others (LmjF.15.1480 and LmjF.27.2030). Our data suggest that these genomic regions probably collapsed during the genome assembly due to the existence of gene duplications and/or repeated regions surrounding the missed genes. Conclusion RNA-seq data helped to reconstruct some genomic regions misassembled during the L. major Friedlin genome assembly, which is otherwise quite robust. On the other hand, this study shows that data derived from massive sequencing approaches, including RNA-Seq, should be carefully inspected to improve current genome definition and gene annotations. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1329-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Graciela Alonso
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás Cabrera, 1, 28049, Madrid, Spain.
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás Cabrera, 1, 28049, Madrid, Spain.
| | - Sara López-Pérez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás Cabrera, 1, 28049, Madrid, Spain.
| | - Jose M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás Cabrera, 1, 28049, Madrid, Spain.
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás Cabrera, 1, 28049, Madrid, Spain.
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